Multimodal CRISPR perturbations of GWAS loci associated with coronary artery disease in vascular endothelial cells

• Published in: PLoS genetics 2023-03, Vol.19 (3), p.e1010680-e1010680
• Main Authors: Wünnemann, Florian, Fotsing Tadjo, Thierry, Beaudoin, Mélissa, Lalonde, Simon, Lo, Ken Sin, Kleinstiver, Benjamin P, Lettre, Guillaume
• Format: Article
• Language: English
• Subjects: Analysis; Atherosclerosis; Bioavailability; Biology and Life Sciences; Calcium signalling; Cardiovascular disease; Care and treatment; Cell cycle; Clustered Regularly Interspaced Short Palindromic Repeats; Coronary artery disease; Coronary Artery Disease - genetics; Coronary Artery Disease - metabolism; Coronary heart disease; Coronary vessels; CRISPR; DEAD-box RNA Helicases - genetics; Design; Diagnosis; Disease prevention; DNA helicase; E-selectin; Endothelial cells; Endothelial Cells - metabolism; Endothelium; Engineering and Technology; Flow cytometry; Genetic aspects; Genetic diversity; Genetic Predisposition to Disease; Genetic variance; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomics; Heart diseases; Humans; Intercellular adhesion molecule 1; Medicine and Health Sciences; Methods; Molecular modelling; Nitric oxide; Physiology, Pathological; Polymorphism, Single Nucleotide - genetics; Proteins; Quantitative Trait Loci; Reactive oxygen species; Research and Analysis Methods; RNA helicase; RNA Splicing Factors - genetics; Senescence; Vein & artery diseases
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1010680

Genome-wide association studies have identified >250 genetic variants associated with coronary artery disease (CAD), but the causal variants, genes and molecular mechanisms remain unknown at most loci. We performed pooled CRISPR screens to test the impact of sequences at or near CAD-associated genetic variants on vascular endothelial cell functions. Using CRISPR knockout, inhibition and activation, we targeted 1998 variants at 83 CAD loci to assess their effect on three adhesion proteins (E-selectin, ICAM1, VCAM1) and three key endothelial functions (nitric oxide and reactive oxygen species production, calcium signalling). At a false discovery rate ≤10%, we identified significant CRISPR perturbations near 42 variants located within 26 CAD loci. We used base editing to validate a putative causal variant in the promoter of the FES gene. Although a few of the loci include genes previously characterized in endothelial cells (e.g. AIDA, ARHGEF26, ADAMTS7), most are implicated in endothelial dysfunction for the first time. Detailed characterization of one of these new loci implicated the RNA helicase DHX38 in vascular endothelial cell senescence. While promising, our results also highlighted several limitations in using CRISPR perturbations to functionally dissect GWAS loci, including an unknown false negative rate and potential off-target effects.